A package for operating Quantum Chemistry programs using qcio standardized data structures. Compatible with TeraChem, psi4, QChem, NWChem, ORCA, Molpro, geomeTRIC and many more.
Project description
Quantum Chemistry Operate
A package for operating Quantum Chemistry programs using qcio standardized data structures. Compatible with TeraChem
, psi4
, QChem
, NWChem
, ORCA
, Molpro
, geomeTRIC
and many more.
qcop
works in harmony with a suite of other quantum chemistry tools for fast, structured, and interoperable quantum chemistry.
The QC Suite of Programs
- qcio - Beautiful and user friendly data structures for quantum chemistry.
- qcparse - A library for efficient parsing of quantum chemistry data into structured
qcio
objects. - qcop - A package for operating quantum chemistry programs using
qcio
standardized data structures. Compatible withTeraChem
,psi4
,QChem
,NWChem
,ORCA
,Molpro
,geomeTRIC
and many more. - BigChem - A distributed application for running quantum chemistry calculations at scale across clusters of computers or the cloud. Bring multi-node scaling to your favorite quantum chemistry program.
ChemCloud
- A web application and associated Python client for exposing a BigChem cluster securely over the internet.
Installation
pip install qcop
Quickstart
qcop
uses the qcio
data structures to drive quantum chemistry programs in a standardized way. This allows for a simple and consistent interface to a wide variety of quantum chemistry programs. See the qcio library for documentation on the input and output data structures.
The compute
function is the main entry point for the library and is used to run a calculation.
from qcio import Molecule, ProgramInput
from qcop import compute
from qcop.exceptions import ExternalProgramError
# Create the molecule
h2o = Molecule.open("h2o.xyz")
# Define the program input
prog_input = ProgramInput(
molecule=h2o,
calctype="energy",
model={"method": "hf", "basis": "sto-3g"},
keywords={"purify": "no", "restricted": False},
)
# Run the calculation; will return SinglePointOutput or raise an exception
try:
output = compute("terachem", prog_input, collect_files=True)
except ExternalProgramError as e:
# External QQ program failed in some way
prog_failure = e.program_failure
prog_failure.input_data # Input data used by the QC program
prog_failure.success # Will be False
prog_failure.results # Any half-computed results before the failure
prog_failure.traceback # Stack trace from the calculation
prog_failure.ptraceback # Shortcut to print out the traceback in human readable format
prog_failure.stdout # Stdout log from the calculation
raise e
else:
# Calculation succeeded
output.input_data # Input data used by the QC program
output.success # Will be True
output.results # All structured results from the calculation
output.stdout # Stdout log from the calculation
output.pstdout # Shortcut to print out the stdout in human readable format
output.files # Any files returned by the calculation
output.provenance # Provenance information about the calculation
output.extras # Any extra information not in the schema
One may also call compute(..., raise_exc=False)
to return a ProgramFailure
object rather than raising an exception when a calculation fails. This may allow easier handling of failures in some cases.
from qcio import Molecule, ProgramInput
from qcop import compute
from qcop.exceptions import ExternalProgramError
# Create the molecule
h2o = Molecule.open("h2o.xyz")
# Define the program input
prog_input = ProgramInput(
molecule=h2o,
calctype="energy",
model={"method": "hf", "basis": "sto-3g"},
keywords={"purify": "no", "restricted": False},
)
# Run the calculation; will return either a SinglePointOutput or a ProgramFailure
output = compute("terachem", prog_input, collect_files=True, raise_exc=False)
if not output.success:
# External QQ program failed in some way
output.input_data # Input data used by the QC program
output.success # Will be False
output.results # Any half-computed results before the failure
output.traceback # Stack trace from the calculation
output.ptraceback # Shortcut to print out the traceback in human readable format
output.stdout # Stdout log from the calculation
else:
# Calculation succeeded
output.input_data # Input data used by the QC program
output.success # Will be True
output.results # All structured results from the calculation
output.stdout # Stdout log from the calculation
output.pstdout # Shortcut to print out the stdout in human readable format
output.files # Any files returned by the calculation
output.provenance # Provenance information about the calculation
output.extras # Any extra information not in the schema
Alternatively, the compute_args
function can be used to run a calculation with the input data structures passed in as arguments rather than as a single ProgramInput
object.
from qcio import Molecule
from qcop import compute_args
# Create the molecule
h2o = Molecule.open("h2o.xyz")
# Run the calculation
output = compute_args(
"terachem",
h2o,
calctype="energy",
model={"method": "hf", "basis": "sto-3g"},
keywords={"purify": "no", "restricted": False},
files={...},
collect_files=True
)
The behavior of compute()
and compute_args()
can be tuned by passing in keyword arguments like collect_files
shown above. Keywords can modify which scratch directory location to use, whether to delete or keep the scratch files after a calculation completes, what files to collect from a calculation, whether to print the program stdout in real time as the program executes, and whether to propagate a wavefunction through a series of calculations. Keywords also include hooks for passing in update functions that can be called as a program executes in real time. See the compute method docstring for more details.
See the /examples directory for more examples.
Support
If you have any issues with qcop
or would like to request a feature, please open an issue.
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